Function reference • scCustomize

Read & Write Data Functions for reading and writing single cell sequencing data from raw data files.
`Create_10X_H5()`	Create H5 from 10X Outputs
`Create_CellBender_Merged_Seurat()`	Create Seurat Object with Cell Bender and Raw data
`Pull_Directory_List()`	Pull Directory List
`Read10X_GEO()`	Load in NCBI GEO data from 10X
`Read10X_Multi_Directory()`	Load 10X count matrices from multiple directories
`Read10X_h5_GEO()`	Load in NCBI GEO data from 10X in HDF5 file format
`Read10X_h5_Multi_Directory()`	Load 10X h5 count matrices from multiple directories
`Read_CellBender_h5_Mat()`	Load CellBender h5 matrices (corrected)
`Read_CellBender_h5_Multi_Directory()`	Load CellBender h5 matrices (corrected) from multiple directories
`Read_CellBender_h5_Multi_File()`	Load CellBender h5 matrices (corrected) from multiple files
`Read_GEO_Delim()`	Load in NCBI GEO data formatted as single file per sample
`Read_Metrics_10X()`	Read Overall Statistics from 10X Cell Ranger Count
`Read_Metrics_CellBender()`	Read Overall Statistics from CellBender
Merge Data Utilities Utilities to merge raw data.
`Extract_Modality()`	Extract multi-modal data into list by modality
`Merge_Sparse_Data_All()`	Merge a list of Sparse Matrices
`Merge_Sparse_Multimodal_All()`	Merge a list of Sparse Matrices contain multi-modal data.
Edit Barcode Utilities Utilities to edit cell barcodes
`Change_Delim_All()`	Change all delimiters in cell name
`Change_Delim_Prefix()`	Change barcode prefix delimiter
`Change_Delim_Suffix()`	Change barcode suffix delimiter
`Replace_Suffix()`	Replace barcode suffixes
Sequencing Metrics QC Plots Functions plotting various QC metrics provides by 10X Genomics Cell Ranger Outputs
`Seq_QC_Plot_Alignment_Combined()`	QC Plots Sequencing metrics (Alignment) (Layout)
`Seq_QC_Plot_Basic_Combined()`	QC Plots Sequencing metrics (Layout)
`Barcode_Plot()`	Create Barcode Rank Plot
`Iterate_Barcode_Rank_Plot()`	Iterative Barcode Rank Plots
`Seq_QC_Plot_Genes()`	QC Plots Sequencing metrics
`Seq_QC_Plot_Number_Cells()`	QC Plots Sequencing metrics
`Seq_QC_Plot_Reads_in_Cells()`	QC Plots Sequencing metrics
`Seq_QC_Plot_Reads_per_Cell()`	QC Plots Sequencing metrics
`Seq_QC_Plot_Saturation()`	QC Plots Sequencing metrics
`Seq_QC_Plot_Total_Genes()`	QC Plots Sequencing metrics
`Seq_QC_Plot_UMIs()`	QC Plots Sequencing metrics
`Seq_QC_Plot_Antisense()`	QC Plots Sequencing metrics (Alignment)
`Seq_QC_Plot_Exonic()`	QC Plots Sequencing metrics (Alignment)
`Seq_QC_Plot_Genome()`	QC Plots Sequencing metrics (Alignment)
`Seq_QC_Plot_Intergenic()`	QC Plots Sequencing metrics (Alignment)
`Seq_QC_Plot_Intronic()`	QC Plots Sequencing metrics (Alignment)
`Seq_QC_Plot_Transcriptome()`	QC Plots Sequencing metrics (Alignment)
Basic Analysis QC Plots Functions plotting various QC from Seurat Objects.
`QC_Histogram()`	QC Histogram Plots
`QC_Plot_GenevsFeature()`	QC Plots Genes vs Misc
`QC_Plot_UMIvsFeature()`	QC Plots UMI vs Misc
`QC_Plot_UMIvsGene()`	QC Plots Genes vs UMIs
`QC_Plots_Combined_Vln()`	QC Plots Genes, UMIs, & % Mito
`QC_Plots_Complexity()`	QC Plots Cell "Complexity"
`QC_Plots_Feature()`	QC Plots Feature
`QC_Plots_Genes()`	QC Plots Genes
`QC_Plots_Mito()`	QC Plots Mito
`QC_Plots_UMIs()`	QC Plots UMIs
Seurat Plotting Functions Functions customization and plotting of single cell data/results from Seurat Objects.
`Cell_Highlight_Plot()`	Meta Highlight Plot
`Cluster_Highlight_Plot()`	Cluster Highlight Plot
`Clustered_DotPlot()`	Clustered DotPlot
`DimPlot_All_Samples()`	DimPlot by Meta Data Column
`DimPlot_scCustom()`	DimPlot with modified default settings
`DotPlot_scCustom()`	Customized DotPlot
`FeaturePlot_DualAssay()`	Customize FeaturePlot of two assays
`FeaturePlot_scCustom()`	Customize FeaturePlot
`FeatureScatter_scCustom()`	Modified version of FeatureScatter
`Meta_Highlight_Plot()`	Meta Highlight Plot
`PC_Plotting()`	PC Plots
`SpatialDimPlot_scCustom()`	SpatialDimPlot with modified default settings
`Stacked_VlnPlot()`	Stacked Violin Plot
`VariableFeaturePlot_scCustom()`	Custom Labeled Variable Features Plot
`VlnPlot_scCustom()`	VlnPlot with modified default settings
`Plot_Density_Custom()`	Nebulosa Density Plot
`Plot_Density_Joint_Only()`	Nebulosa Joint Density Plot
Iterative Plotting Functions Functions for quick iterative plotting.
`Iterate_Cluster_Highlight_Plot()`	Iterate Cluster Highlight Plot
`Iterate_DimPlot_bySample()`	Iterate DimPlot By Sample
`Iterate_FeaturePlot_scCustom()`	Iterative Plotting of Gene Lists using Custom FeaturePlots
`Iterate_Meta_Highlight_Plot()`	Iterate Meta Highlight Plot
`Iterate_PC_Loading_Plots()`	Iterate PC Loading Plots
`Iterate_Plot_Density_Custom()`	Iterative Plotting of Gene Lists using Custom Density Plots
`Iterate_Plot_Density_Joint()`	Iterative Plotting of Gene Lists using Custom Joint Density Plots
`Iterate_VlnPlot_scCustom()`	Iterative Plotting of Gene Lists using VlnPlot_scCustom
LIGER Plotting Functions Functions customization and plotting of single cell data/results from LIGER Objects.
`DimPlot_LIGER()`	DimPlot LIGER Version
`Factor_Cor_Plot()`	Factor Correlation Plot
`plotFactors_scCustom()`	Customized version of plotFactors
Plotting Utilities #1 (Color Palettes) Helper functions for quick access to useful or default color palettes.
`ColorBlind_Pal()`	Color Universal Design Short Palette
`Dark2_Pal()`	Dark2 Palette
`DiscretePalette_scCustomize()`	Discrete color palettes
`Hue_Pal()`	Hue_Pal
`JCO_Four()`	Four Color Palette (JCO)
`NavyAndOrange()`	Navy and Orange Dual Color Palette
`PalettePlot()`	Plot color palette in viewer
`Single_Color_Palette()`	Single Color Palettes for Plotting
`scCustomize_Palette()`	Color Palette Selection for scCustomize
`viridis_plasma_dark_high` `viridis_plasma_light_high` `viridis_inferno_dark_high` `viridis_inferno_light_high` `viridis_magma_dark_high` `viridis_magma_light_high` `viridis_dark_high` `viridis_light_high`	Viridis Shortcuts
Plotting Utilities #2 (Themes/Theme Adjustment) Helper functions for quick modification of theme elements and custom themes.
`Blank_Theme()`	Blank Theme
`Move_Legend()`	Move Legend Position
`UnRotate_X()`	Unrotate x axis on VlnPlot
`theme_ggprism_mod()`	Modified ggprism theme
Helper Utilities (Seurat) Functions to provide ease of use for frequently used code from Seurat Objects.
QC Utilities Functions to add common QC variables to meta.data.
`Add_CellBender_Diff()`	Calculate and add differences post-cell bender analysis
`Add_Cell_Complexity()`	Add Cell Complexity
`Add_Cell_QC_Metrics()`	Add Multiple Cell Quality Control Values with Single Function
`Add_Hemo()`	Add Hemoglobin percentages
`Add_Mito_Ribo()`	Add Mito and Ribo percentages
`Add_Top_Gene_Pct()`	Add Percent of High Abundance Genes
Getters/Setters Functions to extract data from or add additional data to Seurat objects
`Add_Alt_Feature_ID()`	Add Alternative Feature IDs
`Add_Sample_Meta()`	Add Sample Level Meta Data
`Extract_Sample_Meta()`	Extract sample level meta.data
`Fetch_Meta()`	Get meta data from object
`Meta_Remove_Seurat()`	Remove meta data columns containing Seurat Defaults
`Random_Cells_Downsample()`	Randomly downsample by identity
`Rename_Clusters()`	Rename Clusters
`Store_Misc_Info_Seurat()`	Store misc data in Seurat object
`Store_Palette_Seurat()`	Store color palette in Seurat object
Check Utilities Functions to check validity of different aspects of object or object contents.
`Case_Check()`	Check for alternate case features
`CheckMatrix_scCustom()`	Check Matrix Validity
`Feature_Present()`	Check if genes/features are present
`Meta_Numeric()`	Check if meta data columns are numeric
`Meta_Present()`	Check if meta data are present
`Reduction_Loading_Present()`	Check if reduction loadings are present
Misc Utilities Miscellaneous Utilities
`Merge_Seurat_List()`	Merge a list of Seurat Objects
`Split_Vector()`	Split vector into list
`Updated_HGNC_Symbols()`	Update HGNC Gene Symbols
`Updated_MGI_Symbols()`	Update MGI Gene Symbols
`seq_zeros()`	Create sequence with zeros
Helper Utilities (LIGER) Functions to provide ease of use for frequently used code from LIGER Objects.
`Add_Cell_Complexity()`	Add Cell Complexity
`Add_Mito_Ribo()`	Add Mito and Ribo percentages
`Cells(<liger>)`	Extract Cells from LIGER Object
`Cells_by_Identities_LIGER()`	Extract Cells by identity
`Embeddings(<liger>)`	Extract matrix of embeddings
`Features(<liger>)`	Extract Features from LIGER Object
`Fetch_Meta()`	Get meta data from object
`Find_Factor_Cor()`	Find Factor Correlations
`Idents(<liger>)` `Idents<-`(<liger>)	Extract or set default identities from object
`Subset_LIGER()`	Subset LIGER object
`Top_Genes_Factor()`	Extract top loading genes for LIGER factor
`Variable_Features_ALL_LIGER()`	Perform variable gene selection over whole dataset
`WhichCells(<liger>)`	Extract Cells for particular identity
Object Conversion Functions Functions to convert between different single cell object formats (R & Python).
`Convert_Assay()`	Convert between Seurat Assay types
`Liger_to_Seurat()`	Create a Seurat object containing the data from a liger object
`Split_Layers()`	Split Seurat object into layers
`as.LIGER()`	Convert objects to LIGER objects
`as.Seurat(<liger>)`	Convert objects to `Seurat` objects
`as.anndata()`	Convert objects to anndata objects
Cluster/Marker Annotation Utilities Functions to provide ease of use or add functionality to DEG and cluster annotation.
`Add_Pct_Diff()`	Add percentage difference to DE results
`Create_Cluster_Annotation_File()`	Create cluster annotation csv file
`Extract_Top_Markers()`	Extract Top N Marker Genes
`Pull_Cluster_Annotation()`	Pull cluster information from annotation csv file.
`Rename_Clusters()`	Rename Clusters
Project Organization Utilities Functions to provide ease of use for organization of analysis projects.
`Copy_From_GCP()`	Copy folder from GCP bucket from R Console
`Copy_To_GCP()`	Copy folder to GCP bucket from R Console
`Setup_scRNAseq_Project()`	Setup project directory structure
Statistics Functions Functions quick return of different object and data metrics.
`CellBender_Feature_Diff()`	CellBender Feature Differences
`Cells_per_Sample()`	Cells per Sample
`Cluster_Stats_All_Samples()`	Calculate Cluster Stats
`MAD_Stats()`	Median Absolute Deviation Statistics
`Median_Stats()`	Median Statistics
`Percent_Expressing()`	Calculate percent of expressing cells
`CellBender_Diff_Plot()`	Plot Number of Cells/Nuclei per Sample
`Plot_Cells_per_Sample()`	Plot Number of Cells/Nuclei per Sample
`Plot_Median_Genes()`	Plot Median Genes per Cell per Sample
`Plot_Median_Mito()`	Plot Median Percent Mito per Cell per Sample
`Plot_Median_Other()`	Plot Median other variable per Cell per Sample
`Plot_Median_UMIs()`	Plot Median UMIs per Cell per Sample
`Proportion_Plot()`	Cell Proportion Plot
Data Reference data for package functions.
`ensembl_hemo_id`	Ensembl Hemo IDs
`ensembl_ieg_list`	Immediate Early Gene (IEG) gene lists
`ensembl_mito_id`	Ensembl Mito IDs
`ensembl_ribo_id`	Ensembl Ribo IDs
`ieg_gene_list`	Immediate Early Gene (IEG) gene lists
`msigdb_qc_ensembl_list`	QC Gene Lists
`msigdb_qc_gene_list`	QC Gene Lists

Reference

Read & Write Data

Merge Data Utilities

Edit Barcode Utilities

Sequencing Metrics QC Plots

Basic Analysis QC Plots

Seurat Plotting Functions

Iterative Plotting Functions

LIGER Plotting Functions

Plotting Utilities #1 (Color Palettes)

Plotting Utilities #2 (Themes/Theme Adjustment)

Helper Utilities (Seurat)

QC Utilities

Getters/Setters

Check Utilities

Misc Utilities

Helper Utilities (LIGER)

Object Conversion Functions

Cluster/Marker Annotation Utilities

Project Organization Utilities

Statistics Functions

Data